Bowtie is a nice tool for short read alignment I think. However, I found a problem in pair-end data mapping. I produced 75bp reads by simulating Illumina's high-throughput sequencing, and aligned them to the reference sequence. By the way, only few alignments, less than 10, are reported. As 1300000 alignments are reported with non paired-end mapping, probably it is wrongly mapped I think.
My option is "bowtie -p 8 -a -y -X 650 human -1 reads_1.fa -2 reads_2.fa output.map".
Can anybody tell me what is the problem?
My option is "bowtie -p 8 -a -y -X 650 human -1 reads_1.fa -2 reads_2.fa output.map".
Can anybody tell me what is the problem?
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